Mitochondria analytics
Visualization and analysis tools for analyzing mitochondria in the Layer 2/3 EM volume
visualize all mitochondria in a cell of interest
Contents
Visualization tools
Visualize a single mitochondrion of interest in Neuroglancer
neuroglancer_link_generator_mitochondria_visualization_version.ipynb:
generate a Neuroglancer link for a single cellid and single
mitochondrion from the
pni_mito_cellswskel_v185_fullstats.csv datatable. The view
will be centered at the centroid of the mitochondrion in the volume.
neuroglancer link to a single mitochondrion with crosshair at the mito centroid
Visualize all mitochondria in a cell of interest in Neuroglancer
neuroglancer_link_generator_all_mitochondria.ipynb:
generate a Neuroglancer link for all the mitochondria in a single cellid
of interest pulling the mito ids from the
211019_mitochondria_info.csv datatable.
neuroglancer link generator for all mitochondria in a cell
3D visualizer of all mitochondria in a cell of interesting using Meshparty, vtk, and OpenGL viewer
vtk_mitochondria_visualizer.ipynb:
generate a 3D interactive view of all mitochondria in a cell of
interest. Note this method has significant file download and space
requirements compared to using the Neuroglancer viewer.
3D visualizer of all mitochondria in a cell
3D visualizer of all mitochondria and synapses in a cell of interesting using Meshparty, vtk, and OpenGL viewer
vtk_mitochondria_visualizer_with_synapses.ipynb:
generate a 3D interactive view of all mitochondria in a cell of interest
along with the pre- and post-syanptic sites. Note this method has
significant file download and space requirements compared to using the
Neuroglancer viewer.
3D visualizer of all mitochondria and synapses in a cell